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TSNAX-DISC1 TSNAX-DISC1 readthrough (NMD candidate) [ Homo sapiens (human) ]

Gene ID: 100303453, updated on 10-Oct-2023

Summary

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Official Symbol
TSNAX-DISC1provided by HGNC
Official Full Name
TSNAX-DISC1 readthrough (NMD candidate)provided by HGNC
Primary source
HGNC:HGNC:49177
See related
Ensembl:ENSG00000270106 AllianceGenome:HGNC:49177
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene represents naturally occurring read-through transcription between the neighboring TSNAX (translin-associated factor X) and DISC1 (disrupted in schizophrenia 1) genes on chromosome 1. Alternative splicing results in multiple transcript variants, all of which are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to be protein-coding. These alterations in gene processing may be associated with risk for psychiatric illness, most notably, schizophrenia. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in placenta (RPKM 3.7), brain (RPKM 2.9) and 25 other tissues See more
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Genomic context

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See TSNAX-DISC1 in Genome Data Viewer
Location:
1q42.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (231528653..232041272)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230911887..231426811)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (231664399..232177018)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr1:231614566-231615067 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:231634962-231635134 Neighboring gene small nuclear ribonucleoprotein D2 pseudogene 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:231647424-231648623 Neighboring gene uncharacterized LOC122526782 Neighboring gene Sharpr-MPRA regulatory region 8140 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:231663972-231665171 Neighboring gene translin associated factor X Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2731 Neighboring gene long intergenic non-protein coding RNA 582 Neighboring gene MPRA-validated peak764 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1955 Neighboring gene MPRA-validated peak765 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231787054-231787554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231787555-231788055 Neighboring gene DISC1 scaffold protein Neighboring gene ReSE screen-validated silencer GRCh37_chr1:231830220-231830402 Neighboring gene RNA, U5A small nuclear 5, pseudogene Neighboring gene MPRA-validated peak767 silencer Neighboring gene uncharacterized LOC105373170 Neighboring gene NANOG hESC enhancer GRCh37_chr1:231967105-231967615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1956 Neighboring gene disrupted in schizophrenia 2 Neighboring gene DISC1 intronic transcript 1 Neighboring gene uncharacterized LOC124904549 Neighboring gene NANOG hESC enhancer GRCh37_chr1:232173754-232174300 Neighboring gene uncharacterized LOC105373172 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:232179763-232180962 Neighboring gene uncharacterized LOC105373171 Neighboring gene MPRA-validated peak768 silencer

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Impact of DISC1 variation on neuroanatomical and neurocognitive phenotypes. Carless MA, et al. Mol Psychiatry, 2011 Nov. PMID 21483430, Free PMC Article
  2. DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms. Nakata K, et al. Proc Natl Acad Sci U S A, 2009 Sep 15. PMID 19805229, Free PMC Article
  3. Association of DISC1 and TSNAX genes and affective disorders in the depression case-control (DeCC) and bipolar affective case-control (BACCS) studies. Schosser A, et al. Mol Psychiatry, 2010 Aug. PMID 19255581
  4. Chromosomal location and genomic structure of the human translin-associated factor X gene (TRAX; TSNAX) revealed by intergenic splicing to DISC1, a gene disrupted by a translocation segregating with schizophrenia. Millar JK, et al. Genomics, 2000 Jul 1. PMID 10945471
  5. Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. Beecham GW, et al. Am J Hum Genet, 2009 Jan. PMID 19118814, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Association between single nucleotide polymorphism-genotype and outcome of patients with chronic lymphocytic leukemia in a randomized chemotherapy trial.
EBI GWAS Catalog
Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease.
EBI GWAS Catalog
Impact of DISC1 variation on neuroanatomical and neurocognitive phenotypes.
EBI GWAS Catalog
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_028393.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the longest transcript, which is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804217

  2. NR_028394.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several 3' exons, but has two additional exons in the 5' and 3' regions respectively and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804219
    Related
    ENST00000602962.5

  3. NR_028395.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks several 3' exons, but has an additional exon in the 5' region, an alternate exon in the 3' region and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804220
    Related
    ENST00000602567.1

  4. NR_028396.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several 3' exons, but has an additional exon in the 3' region and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804218
    Related
    ENST00000602634.5

  5. NR_028397.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) This variant (5) lacks an internal exon and several 3' exons, but has two additional exons in the 5' and 3' regions respectively and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804221
    Related
    ENST00000602956.5

  6. NR_028398.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two internal exons in the 5' region and several 3' exons, but has two additional exons in the 5' and 3' regions respectively and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804222
    Related
    ENST00000602885.5

  7. NR_028399.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks multiple 3' exons but has two additional exons in the 5' region and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804224

  8. NR_028400.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) lacks an internal exon and multiple 3' exons but has an additional exon in the 5' region and an alternate 3' segment, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, and is unlikely to make a functional protein.
    Source sequence(s)
    FJ804223
    Related
    ENST00000647072.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    231528653..232041272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    230911887..231426811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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